Where Loyalties Lie
by August08
Summary: Micaiah had always known what her purpose in life was: Bring her master's enemies to their demise. However, when fate turns and she finds herself as the guest of the very ones she was trained to kill, her very existence is questioned. And when a certain blue masked turtle begins to steal her heart, she must choose where her loyalties truly lie.
1. Chapter 1

**A/N**: A couple years back I wrote a story called Counterpart. I didn't like how that story was turning out so I took it down and revamped it. This is what was born.

**Disclaimer**: I own nothing, only the OCs

* * *

_The ticking of the implosion bomb sounded like an explosion. Time was running out. Shredder had sent Hun and the Foot Elite after Stockman, and Leonardo vaguely noticed Hun pause briefly at the door of the transmat room before disappearing outside. However, he didn't see why Hun paused since Shredder was standing in his line of sight. Leonardo tightened his grip on his swords and glared at his enemy. He felt the presence of his family around him and he knew he wasn't fighting alone. Shredder sprang forward, knocking Leonardo and Splinter out of his way before throwing Raphael to the side. The red masked turtle collided with Donatello and both brothers collapsed to the floor._

_Shredder stalked up the steps to the platform, murder and malice blazing in his eyes. Then, the mutant family was on him again. With a battle cry they pushed Shredder back away from Mortu and the Guardians. As his family fought to keep Shredder at bay, Donatello powered up the transmat and sent the remaining Guardians and Utroms home._

"Leeeooo!" Michelangelo's voice rang out.

Leonardo cracked an eye open, annoyed that his mediation had been interrupted. He looked over his shoulder to see Michelangelo appear in the doorway of his room wearing a "Kiss The Cook" apron.

"Yes, Mikey?" Leonardo asked as patiently as he could.

"Supper's ready," Michelangelo said. "You've been meditating all day. Your brain is going to turn to mush."

Leonardo stood up and headed for the door. "Meditation doesn't turn brains to mush, Mikey," he replied as he led his brother down to the kitchen.

Michelangelo followed close behind him. "What were you meditating about, anyway?" he wanted to know.

"Our fight with the Shredder in TCRI," Leonardo answered. "There's something about it that's been bothering me."

The brothers entered the kitchen. Raphael, Donatello and Splinter were already sitting at the table.

"You mean how we almost got imploded?" Michelangelo asked. "And dropped out of the sky on to the Battle Shell?" He gave Donatello a quick glare. "No thanks to Donnie."

Leonardo shook his head. "No, not that. Something Hun did."

"He ran with his tail between his legs," Raphael said. "What more is there?"

Leonardo pulled out his chair and sat down as Michelangelo laid out plates of food on the table in front of his family. "I saw him pause at the door. Why would he do that when there was danger and he had been given a direct order?" he asked.

"Too many questions and not enough answers," Splinter commented. "Such questions are best left for later, when the mind is clear and focused. Right now, we eat and enjoy each other's company. Trials and troubles can wait."

Leonardo inclined his head. "Yes, Master Splinter. Sorry," he apologized.

He looked down at his plate to find it piled high with a hot turkey supper which was smothered in gravy.

"There's lots there. So help yourselves to seconds," Michelangelo said as he sat down next to Leonardo.

Everyone ate in silence with only the clicking of forks and knives on plates to break it. It wasn't everyday that they got to enjoy a turkey supper, and when they did they savoured every mouthful. Raphael took a sip of soda and put a hand over his mouth as he let out a small belch. It was followed by a hiccup from Donatello.

"No one's gonna take your food from ya, Donnie," Raphael commented. "Slow down."

Michelangelo grinned. "I take it as a compliment," he said.

Leonardo stabbed his fork in a bit of cabbage and popped it into his mouth. He looked around at his family and smiled. Nothing could ruin this moment. He pushed the memory of the TCRI fight to the back of his mind and enjoyed the company of his family. Whatever was happening in the world could wait. What kind of trouble could happen in a few short hours?

* * *

It had been a simple plan. When he had discovered what Hun did before escaping TCRI, Shredder ordered Stockman to modify the mutagen to his specifications. Of course, no one asked how he knew the mutagen could be modified in the first place. They just chalked it up to their leader knowing the most of the Utrom's technology after years of research and study.

What they weren't expecting was the command to find four normal, everyday turtles. The one most confused by this request was Karai. When the turtles had been brought to the genetics lab, she approached her mentor.

"Master, if I may ask. Why mutate the very species that has been giving you trouble?" Karai asked.

"I know now that if you want to catch a turtle, send a turtle," Shredder answered.

The mutagen had been modified to speed up the growing process to take only a matter of months. However, the learning process was still the same. But even then, the four newly mutated turtles showed signs of intelligence, even at an early age. They weren't as advanced yet as the Shredder's enemies, but they were advanced enough to be trained. Karai was tasked with training them herself. Teaching them everything from the alphabet to the first stages of ninjitsu.

Now all that hard work was finally going to be paid off. Karai just had to make sure that her students were ready. They had one final test to prove themselves before they could be sent out to hunt down the Turtles. So here she knelt in the darkened dojo, listening for the faintest of sounds. Karai strained her ears, holding her breath so she could hear more clearly.

A faint breath; the clinking of metal.

_Duck._

Karai dodged the first attack; the weight of a manriki chain sailing over her head. She grabbed the chain and spun to her feet, pulling on the chain as she did so. The owner of the weapon stumbled into view. Wide, green eyes shone through the black eye mask. Before Karai could deliver a damaging blow, the turtle released their grip on the other end of the chain and vanished back into the darkness of the shadows. Karai dropped the chain to the floor and looked around. There was the sound of a string being pulled taut.

_The beams,_ Karai thought. _Up above._

They weren't doing a very good job of keeping hidden. Karai felt something slice the air beside her head, which was followed by the sound of an arrow piercing wood. She shook her head in disapproval. Even in the dark, a skilled archer would have hit their mark. Karai was getting disappointed. She had hoped that her students would have been better suited for this test.

Footsteps pounded across the padded floor. Karai sighed. The assailant wasn't even trying to hide. Karai dodged to the side as a katar was swung at her head. She ducked as a second came close to catching her in the neck. Karai looked up and could see a dark shape fast approaching in front of her. She reached up and grabbed the first assailant's wrists and threw the startled turtle over her head. The two bodies collided and fell to the floor. The remaining two appeared to avenge their fallen comrades. Unfortunately, they didn't last long.

Karai walked over to the wall and flipped on the light switch. She looked down at the four groaning turtles. She crossed her arms over her chest. One turtle looked up and glared at her with intense indigo eyes.

"Glare at me all you want, Reva," Karai said. "It does not change anything."

"Would've worked out great if Micaiah hadn't blown our cover," Reva grumbled.

Karai closed her eyes and sighed. It was just her luck that the scouts had brought back four female turtles.

_And I thought the male ones were moody,_ Karai thought.

"Sorry," Micaiah apologized as she got to her feet.

"And why are you always apologizing?" another turtle, Tylar asked impatiently. "It makes you sound weak and pathetic."

"Leave her alone, guys," the fourth, Chris said.

Tylar turned on her sister. "And you. Stop sticking up for her."

Chris walked up to Tylar and looked down at her, her grey-blue eyes blazing. "Just because we're Foot ninjas doesn't mean we have to be heartless. So, why don't you go pull that stick out of your butt before you pick a fight with someone bigger than you."

Karai rubbed her eyes. If only they could fight enemies as well as they fought each other. Karai turned and left the dojo, leaving the sisters to argue among themselves. Ready or not, the sisters would soon be sent out to find the Turtles. Karai just hoped that they wouldn't end up killing each other before they could bring their male counterparts to the Shredder.

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Reviews are welcome, flames are not


	2. Chapter 2

Micaiah looked at her reflection in the mirror, safely tucked away in her room with the door shut and locked so no one could disturb her. She had to be the worst ninja in the history of ninjitsu. She was always the first to get caught in training, and even when she wasn't she always ended up giving away the positions of her sisters. It was a wonder Shredder hadn't terminated her himself. Micaiah looked at the symbol emblazoned on the sleeve of her uniform and could feel heat burn behind her eyes. She was an embarrassment to the Foot clan.

A knock on the door snapped Micaiah out of her depressing thoughts. She wiped the tears from her eyes and regained her composure. She cleared her throat, making sure that her voice didn't sound shaky.

"Who is it?" she called out.

"It's Chris. May I come in?"

Micaiah walked over to the door, unlocked it and twisted the handle, swinging the door open. Chris stood outside, looking sympathetic. Micaiah stepped to the side to allow her sister entry into the room. Chris stepped inside and the door was closed behind her.

"How are you holding up?" she asked.

Micaiah shrugged. "I should be used to it, by now," she replied. "Always being the screw up."

"You're not a screw up," Chris argued.

"Everyone else thinks I am," Micaiah put in, walking over to the bed and sitting down.

Chris walked over and sat down beside her sister. "I don't," she said.

"Then you're the only who doesn't," Micaiah said.

"You just have a harder time grasping the skills. No one expects you to get it right the first time," Chris explained.

"Shredder does," Micaiah pointed out, her voice wavering a bit.

Chris put an arm around her sister's shoulders. "Mika, listen to me. Forget about what anyone else thinks. Isn't it enough that the only person who matters thinks you're awesome?"

Micaiah smiled slightly. "You're just saying that to make me feel better."

"It's us against them," Chris said. "Always has been. Tylar and Reva can think what they like. They don't matter."

Micaiah's smile faded. "That's a bad thing to say about your own sisters," she commented.

Chris shrugged. "For all we know we might not even be blood related," she pointed out.

"So, does that mean you and me aren't blood related?" Micaiah asked, not being able to help the horror in her voice.

Chris shook her head. "Naw, the two of us are. What I should have said was that we may not be _brain related_ to Tylar and Reva," she corrected herself.

Micaiah burst out laughing. Chris smiled. She tapped her sister on the shoulder.

"Come on, let's get out of here," Chris said.

Micaiah looked up, wiping tears from her eyes. "What?" she asked.

Chris got to her feet and headed for the changing curtain in the corner. Once behind it, she began removing her uniform and pulled on elbow pads, knee pads, wrist guards and shin guards. As she stepped around the curtain, Chris snapped a belt around her waist.

"Do we have authorization to go out?" Micaiah asked.

"No," Chris replied.

Micaiah blinked. "Well, at least you're honest," she commented.

"We were going to get sent out anyway," Chris pointed out. "We're just speeding up the process."

Micaiah shrugged and got up from the bed. Chris waited patiently as her sister got changed. The only thing they didn't change was their black masks.

_Don't want the Foot mistaking us for the guy turtles,_ Chris thought.

With their weapons secured, the sisters began the long trek of sneaking out of Foot Tower.

* * *

"Tell me again why we're out here?" Michelangelo asked in boredom.

"Leo," Donatello and Raphael replied in unison, equally as bored.

"Right," Michelangelo said. He looked around. "Where _is_ Leo?"

As if to answer his question, a water balloon nailed him in the face. Michelangelo spit water out of his mouth. Raphael whipped out his sais and punctured a balloon before it could hit him. Donatello pulled out his staff and looked around, but no one was there. The brothers went back to back.

"Do you see him?" Michelangelo whispered.

"Stealth trainin'," Raphael said.

"Last one left standing gets out of doing chores for a week?" Donatello challenged with a grin.

Raphael returned it with a smirk. "Sounds good to me," he accepted.

"Count me in," Michelangelo chimed.

With that, the brothers split up and ran for cover.

* * *

"Thanks, Chris," Micaiah said.

"For what?" Chris asked.

"For getting me out of the tower. I was going downhill fast," Micaiah replied.

Chris smiled and threw an arm around her sister's shoulders. "Everything will work out, Mika. You just got to give it time."

"That's the thing: I've been giving it time. But it seems the harder I try, the more I mess things up," Micaiah explained.

Chris tilted her head in a quizzing manner. "Is there something else that's going on?" she asked.

Micaiah looked away, but didn't answer. Chris was about to say something, but movement in the corner of her eye stopped her. She turned to see what had caught her attention. She blinked in surprise. On the next rooftop over the turtle brothers were engaged in a what looked like a water balloon fight. Even from where she was standing, Chris could hear their laughter.

"They look like they're having fun," Micaiah commented.

"Too bad we have to ruin it," Chris said, a bit too cheerfully.

"Yeah," Micaiah sighed regretfully. "Too bad." She looked up her sister. "Do we have to do that now?"

Chris frowned and glanced down at her. "Why are you hesitating? Shredder told us if we were out and we ever ran into the brothers to immediately bring them in. You know that."

Micaiah seemed to shrink into her shell. "I know," she said. "It's just that...they're having so much fun and I don't want to spoil it."

Chris rolled her eyes. "You always were the soft-hearted one," she muttered.

Micaiah took a hold of Chris's arm and tried to pull her away. "We can just walk away and pretend we didn't them. Just this once. Who has to know?" she asked.

Chris's eyes began to wide at something behind her sister. "Um...them?" she guessed, pointing behind Micaiah.

The younger of the two turned around and yelped when she saw Foot ninjas slip out of the shadows. Chris smiled nervously and pulled Micaiah close to her chest.

"Hey, guys. We were just on our way to apprehend the brothers," Chris said. She swallowed when the ninjas pulled out their weapons. "Are you here to assist?"

"I don't think they are," Micaiah whispered as the ninjas surrounded them.

Chris released her hold on her sister's arms and pulled out her spear staff. Micaiah released her manriki chains from the guards on her forearms. The sisters went back to back, trying to keep as many ninjas as they could in their line of sight.

"I told you we should have gotten authorization," Micaiah complained.

Chris growled low in her throat. "No use whining about it now," she said.

Without a word, the Foot ninjas charged. With a battle cry, the sisters ran forward and met their attackers. The night rang with the sounds of clashing steel. Micaiah twirled around, whipping the chains around herself and catching several ninjas. They crumpled to the ground. Chris spun her staff out in front of her. The men she was fighting stumbled back, dazed. She was so caught up in her own battle she lost sight of her sister. That is until she heard Micaiah's scream. Chris shot around just in time to see her little sister disappear over the side of the roof.

"Mika!" Chris screamed.

* * *

Reviews are welcome, flames are not


	3. Chapter 3

**Disclaimer**: see chapter one

* * *

"Mika!" someone screamed.

The brothers stopped their water fight and looked around for the source of the scream. Leonardo turned just in time to see someone fall off the building a couple rooftops away with another getting swarmed by Foot ninjas. Immediately, his instincts kicked in and he dropped the balloon he was about to throw; running towards the fight. His brothers were right behind him.

Chris pushed a few ninjas back, but she was quickly losing the fight. She looked over her shoulder, expecting to see Micaiah climb back up on to the roof; but her sister never appeared. Out of the corner of her eye, Chris could see the brothers fast approaching. She swung her staff, clearing an escape path. She had to get out before she was spotted by the brothers.

_Just have to hope that Mika gets back to the tower okay,_ Chris thought as she bolted back towards Foot Tower.

Seeing the brothers approaching, the Foot ninjas disappeared into the night. Raphael growled in annoyance. He looked around, but the ninjas were gone.

"Cowards!" he yelled to the empty air.

"Strange that we didn't hear anything," Donatello commented.

Leonardo looked around and wandered over to the side of the roof. "Who could hear over Mikey's girly screams?" he asked, looking down into the alley below.

Michelangelo crossed his arms. "Hey, the water was cold," he protested.

Leonardo gasped. "Guys! In the alley. Someone's hurt."

The brothers climbed down the fire escape and landed in the alley. But when they saw who and what the injured person was, they stopped dead.

"Oh," was all Raphael could manage to utter.

"Dudes!" Michelangelo exclaimed. "It's a girl! A girl turtle!"

Donatello cringed. "Yes. Thank you, Captain Obvious, we're aware that she's a girl turtle," he said, stooping down to assess the female for injures.

Leonardo shook himself from the shock. He noticed the black mask around the girl's eyes, but he didn't say anything.

"What's the damage, Don?" Raphael asked.

"Apart from the bump on the back of her head, she's relatively unharmed," Donatello explained. "But, I would like to take her back to the lair for further analysis."

Leonardo blinked. "We can't bring a stranger into the lair," he objected.

Donatello looked up at him. "Uh...April was a stranger and we brought her into the lair," he pointed out. "Besides, this girl's hurt. She needs medical attention. And I can't give that here."

"Come on, Leo, please?" Michelangelo begged. "How many days do we get to meet a girl? A girl that doesn't run away screaming whenever she's sees us."

"He has a point," Raphael reluctantly agreed.

Leonardo sighed in resignation. "Alright, fine. But, Donnie, she's under your watch," he said.

Donatello smiled and carefully picked the injured girl up in his arms. "Let's get back to the lair. She may have a concussion."

The brothers made their way to the manhole cover at the end of the alley. Raphael picked up the cover and allowed his siblings to go down first before following them into the sewers. Every so often, Donatello would glance down at the girl in his arms to make sure she was still okay. She would moan or groan in pain, giving Donatello the answer to his silent question. As soon as he passed over the threshold of the lair, Donatello headed straight for the infirmary. The others waited outside, giving their brother space to work.

"You think she's going to be okay?" Michelangelo asked worriedly.

"Only time will tell, I guess," Leonardo replied.

The brothers turned when they heard the door of Splinter's room slide open. The ninja master appeared in the doorway.

"Back so soon, my sons?" Splinter asked, making his way over to where his sons were standing.

"Something came up, sensei," Leonardo replied.

"A major something," Raphael put in.

Splinter looked from Raphael to Leonardo, his eyes asking for an explanation. Knowing the look in their father's eyes, the turtles parted and Leonardo motioned towards the infirmary.

"It's best if you see for yourself," the blue masked turtle said.

Splinter headed for the infirmary and stepped inside. He blinked in surprise when he saw the female turtle lying on one of the beds. Her head, abdomen, hands and right arm were bandaged. Leonardo, Raphael and Michelangelo walked up behind their father.

"This explains the strange presence I felt," Splinter spoke softly as he made his way over to the occupied bed. He looked up at his sons. "What happened?" Splinter asked.

"From what I saw she and one other were attacked by a group of Foot ninjas," Leonardo explained. "It looked like she was pushed off the roof."

"We couldn't just leave her," Donatello said. "She was injured and needed help."

Splinter held up a hand, silencing his son. "I understand, Donatello. How badly was she hurt?"

"She's suffering from a concussion, cracked ribs and a fractured arm. I'm not sure when she'll wake up," Donatello replied. "The good news is she's responsive to pain and noise."

Michelangelo scratched his head in confusion. "How is that good?" he asked.

"It means she ain't dead, genius," Raphael told him.

"I'm surprised she isn't," Leonardo said, crossing his arms and looking at the girl's still face. "She's lucky the injuries she sustained were the only ones she got; especially after falling ten stories."

"Her shell took the brunt of the fall," Donatello explained. "But, I agree with you, Leo. She should have more injuries."

Splinter looked up at Donatello. "Do you have a theory why she is not more seriously injured?" he asked.

Donatello hummed in thought. "She might have been able to grab hold of the fire escape on her way down," he theorized. "During my examination I noticed that the backs of her hands were cut."

Raphael growled. "So someone forced her to fall," he hissed.

"Seems so," Donatello agreed.

Leonardo continued to study the female turtle as his family talked. She seemed harmless enough; but that could be because she was out cold. Leonardo knew from experience that you never judged someone from their outward appearance. Even though this turtle looked innocent and harmless on the outside, she could very well be a lethal killer on the inside. Leonardo felt his stomach twist at the thought that a potential assassin could be among them. Maybe pushing her off the roof was the only way the Foot were able to get rid of her.

Leonardo mentally shook himself and took a calming breath. _Settle down, Leo,_ he told himself. _Wait and see what happens when she wakes up. When she's awake she'll be able to tell you what you need to know._

* * *

Chris hurried into the dojo to find Tylar and Reva training. They looked calm despite their little sister being missing. In fact, they were a bit too calm. Chris walked over to her sisters, anger flaring.

"Mika's missing and you're still here?" she asked incredulously.

Tylar briefly looked up from adjusting her bow. "Why should we worry?"

Chris frowned in confusion. "She was pushed off a ten story building," she said.

"We know," Reva replied, pounding away at the punching bag.

Chris looked from Tylar to Reva. "You...know? But, how?" Realization dawned on her. "Unless..." Chris trailed off. "You ordered the attack."

Tylar and Reva glanced at each other, giving Chris all the answer she needed.

"She's your sister and you ordered for her to be pushed off a roof?!" Chris yelled.

"It was a necessary evil," Tylar told her, going back to her bow.

"How could you?!" Chris cried.

Reva turned to face her sister. "Face it, Chris. Mika's the weakest of the four of us. She was the obvious choice."

"For what? To be murdered?" Chris asked.

Tylar rolled her eyes. "She's not dead. I made it very clear that she wasn't to be seriously harmed, but just enough so that it wouldn't be too obvious that she's there as our spy."

Chris looked at her sisters with a loathing look in her eyes. "You could have told us," she seethed.

"And then it would have been obvious that the attack was staged," Tylar said. "You guys going out without authorization was the perfect opportunity."

"But Mika doesn't know she's there as a spy," Chris pointed out. "She won't know what to look for."

Tylar grinned darkly. "Oh, she'll know. She'll know everything. And over time, so will we."

She notched an arrow, pulled the string taut and let the arrow fly. It struck dead center in the target at the other end of the room. Tylar looked up at Chris, a dark mirth shining in her blue eyes.

"We will accomplish what the Foot have failed to do," she said. "The young, innocent damsel-in-distress will be the Turtles' downfall."

* * *

Reviews are welcome, flames are not


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